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- __builtin__.object
-
- Atom
- Bond
- Molecule
class Atom(__builtin__.object) |
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Class for describing atoms.
An atom can be a part of a bond.
The following read-only properties are exposed :
index -- one-based index of the atom
coord -- coordinates of the atom (one-based ndarray)
element -- element for the atom (pyviblib.util.pse.Element)
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Methods defined here:
- __init__(self, index, coord, element)
- Constructor of the class.
Positional arguments :
index -- one-based index of the atom
coord -- coordinates of the atom (one-based ndarray)
element -- element for the atom (pyviblib.util.pse.Element)
Data and other attributes defined here:
- __dict__ = <dictproxy object>
- dictionary for instance variables (if defined)
- __weakref__ = <attribute '__weakref__' of 'Atom' objects>
- list of weak references to the object (if defined)
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class Bond(__builtin__.object) |
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Class for describing bonds.
A bond is made up of two atoms and can be a part of a molecule.
The following read-only properties are exposed :
atom1 -- first atom comprising the bond
atom2 -- second atom comprising the bond
is_hydrogen -- whether it is a hydrogen bond
The following public methods are exposed :
length()
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Methods defined here:
- __init__(self, atom1, atom2, is_hydrogen=False)
- Constructor of the class.
Positional arguments :
atom1 -- first atom comprising the bond (Atom)
atom2 -- second atom comprising the bond (Atom)
Keyword arguments :
is_hydrogen -- whether it is a hydrogen bond (default False)
- __str__(self)
- Text description of the bond.
- length(self)
- Calculate the bond length.
Data and other attributes defined here:
- __dict__ = <dictproxy object>
- dictionary for instance variables (if defined)
- __weakref__ = <attribute '__weakref__' of 'Bond' objects>
- list of weak references to the object (if defined)
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class Molecule(__builtin__.object) |
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Class for describing molecules.
A molecule consists of atoms and bonds.
The bonds can be automatically generated from the cartesian coordinates of
the atoms.
The following read-only properties are exposed :
parser -- parser object used to create the molecule
elements -- elements for the atoms
(one-based list of pyviblib.util.pse.Element)
masses -- masses (a.m.u.) of the atoms (one-based ndarray)
atoms -- atoms (null-based list of Atom)
Natoms -- number of atoms (int)
bonds -- bonds (null-based list of Bond)
bonds_matrix -- matrix of the bonds (one-based ndarray)
If a bond between atoms a and b exists, then
bonds_matrix[a, b] = 1
nrot -- number of rotational degrees of freedom (int)
the properties below are set if the normal modes are available :
(tr/rot is an abbreviated form of translations/rotations)
NFreq -- number of frequencies (int, -1 unless set)
Lx -- cartesian excursions (one-based ndarray)
shape : (1 + NFreq, 1 + Natoms, 4)
Lx_norm -- normalized cartesian excursions (one-based ndarray)
shape : (1 + NFreq, 1 + Natoms, 4)
L_tr_rot -- mass-weighted excursions for tr/rot
(one-based ndarray)
shape : (4 + nrot, 1 + Natoms, 4)
Lx_tr_rot -- cartesian excursions for tr/rot
(one-based ndarray)
shape : (4 + nrot, 1 + Natoms, 4)
Lx_tr_rot_norm -- normalized cartesian excursions for tr/rot
(one-based ndarray)
shape : (4 + nrot, 1 + Natoms, 4)
hessian -- hessian (one-based ndarray)
shape : (1 + Natoms, 4, 1 + Natoms, 4)
The following readable and writable properties are exposed :
coords -- cartesian coordinates (one-based ndarray)
shape : (1 + Natoms, 4)
name -- name of the molecule (string)
raman_roa_tensors -- Raman/ROA tensors (set if the data available)
(pyviblib.calc.spectra.RamanROATensors)
ir_vcd_tensors -- IR/VCD tensors (set if the data available)
(pyviblib.calc.spectra.IRVCDTensors)
the properties below are set if the normal modes are available :
freqs -- wavenumbers of the vibrations in cm**(-1)
(one-based ndarray)
L -- mass-weighted excursions (one-based ndarray)
shape : (1 + NFreq, 1 + Natoms, 4)
The following public methods are exposed :
update_masses()
distance()
angle()
dihedral()
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Methods defined here:
- __eq__(self, mol)
- Overloaded version of the comparison operator.
Two Molecule objects are considered to be equal if their elements,
coordinates and the normal modes are the same.
Positional arguments :
mol -- object to compare with
- __init__(self, parser)
- Constructor of the class.
Positional arguments :
parser -- parser object
(subclass of pyviblib.io.parsers.AbstractFileParser)
- angle(self, i1, i2, i3)
- Return the angle in grad between atoms.
Positional arguments :
i1 -- one-based index of the first atom
i2 -- one-based index of the second atom
i3 -- one-based index of the third atom
- dihedral(self, i1, i2, i3, i4)
- Return the dihedral angle in grad between atoms.
Positional arguments :
i1 -- one-based index of the first atom
i2 -- one-based index of the second atom
i3 -- one-based index of the third atom
i4 -- one-based index of the fourth atom
- distance(self, i1, i2)
- Return the distance between atoms.
Positional arguments :
i1 -- one-based index of the first atom
i2 -- one-based index of the second atom
- update_masses(self, data_pairs)
- Modify the masses of atoms.
Positional arguments :
data_pairs -- information about the atoms (null-based ndarray)
shape : (Natoms_to_modify, 2)
atom numbers are one-based
Example :
a1 new_mass1
a2 new_mass2
Data and other attributes defined here:
- __dict__ = <dictproxy object>
- dictionary for instance variables (if defined)
- __weakref__ = <attribute '__weakref__' of 'Molecule' objects>
- list of weak references to the object (if defined)
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